Contacts of the strand formed by residues 35 - 41 (chain A) in PDB entry 1PYB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 5.0 4.3 - - + -
26A GLU 4.1 2.9 - - - +
33A LYS* 3.1 4.0 - - - -
34A LEU* 1.3 85.4 - - + +
36A LYS* 1.3 60.0 + - - +
37A LEU* 2.9 18.3 + - + +
48A VAL 3.3 0.2 - - - +
49A VAL* 3.3 1.5 - - - -
50A ALA* 2.8 44.8 + - + +
51A GLY 4.0 11.2 - - - +
52A ILE* 4.0 22.9 - - + +
56A TYR 4.0 8.5 - - - +
58A PRO* 4.2 23.8 - - + -
61A LEU* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A SER 3.7 0.2 - - - +
25A ALA* 3.4 3.3 - - - -
26A GLU* 3.0 63.0 + - + +
27A ARG 5.4 1.0 + - - -
28A VAL* 3.6 29.3 - - + +
34A LEU* 2.6 17.0 + - - +
35A LEU* 1.3 66.5 - - - +
37A LEU* 1.3 63.5 + - - +
38A THR* 3.5 2.4 + - - +
47A THR* 5.6 4.9 - - - -
48A VAL 3.7 6.1 - - - -
49A VAL* 3.9 22.4 - - + +
81A GLU* 3.4 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.7 36.3 - - + -
24A SER 3.6 2.0 - - - -
25A ALA* 3.9 15.3 - - + -
35A LEU* 2.9 16.2 + - + +
36A LYS* 1.3 69.7 - - - +
38A THR* 1.3 60.9 + - - +
39A LEU* 3.2 13.4 + - + +
46A ARG 3.6 0.9 - - - +
47A THR* 3.6 1.0 - - - -
48A VAL 2.8 34.2 + - - +
50A ALA* 3.8 22.2 - - + -
52A ILE* 5.6 1.8 - - + -
61A LEU* 3.7 33.0 - - + -
66A ILE* 4.4 10.5 - - + -
86A ILE* 3.9 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.3 1.8 - - - +
23A LEU* 2.9 34.8 + - - +
24A SER* 2.8 47.4 + - - +
26A GLU* 4.7 13.0 - - + +
36A LYS 4.5 4.5 - - - +
37A LEU* 1.3 68.8 - - - +
39A LEU* 1.3 64.2 + - - +
45A GLU* 6.4 1.6 - - - -
46A ARG 3.7 4.9 - - - +
47A THR* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 4.0 15.9 - - + +
21A LYS 3.7 2.5 - - - -
22A VAL* 3.9 24.9 - - + -
23A LEU* 5.2 0.4 - - - -
37A LEU* 3.2 13.0 + - + +
38A THR* 1.3 72.3 - - - +
40A SER* 1.3 60.4 + - - +
41A LEU* 3.7 9.1 + - + +
45A GLU* 3.4 5.0 - - - +
46A ARG* 2.9 39.4 + - + +
48A VAL* 3.4 33.0 - - + -
66A ILE* 5.0 4.5 - - + -
68A ILE* 3.4 45.5 - - + -
83A GLN 5.5 0.9 - - - +
86A ILE* 4.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 3.3 12.5 - - - +
21A LYS* 2.9 24.9 + - - +
23A LEU* 3.7 28.9 - - - +
39A LEU* 1.3 72.3 - - - +
41A LEU* 1.3 56.3 + - - +
42A GLY 2.9 11.4 + - - -
44A GLU 3.4 6.3 - - - -
45A GLU* 4.6 4.0 - - - +
106A GLU* 3.3 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.9 37.7 + - + +
19A VAL 4.2 1.3 - - - +
20A ALA* 3.3 24.2 - - + -
39A LEU* 3.7 11.4 + - + +
40A SER* 1.3 67.4 - - - +
42A GLY* 1.3 58.2 + - - +
43A ASP 2.9 9.8 + - - -
44A GLU* 2.7 35.5 + - + +
46A ARG* 3.7 46.2 - - + +
68A ILE* 5.3 9.0 - - + -
70A ALA* 4.6 11.2 - - + -
83A GLN 5.5 1.1 - - - +
107A GLY* 4.2 10.4 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il